Australia's role in the covert US drone strike programme in the Middle East and south Asia should be investigated as part of an ongoing UN inquiry into the use of drones in the "war on terror", two leading Australian human rights groups have said.

A letter seen by Guardian Australia to the UN's special rapporteur on counter-terrorism from the newly opened bureau of Human Rights Watch in Australia and the Human Rights Law Centre in Melbourne says a joint Australian-American intelligence base in the Northern Territory that allegedly supplies geolocation data for strikes on al-Qaida and Taliban militants could violate international human rights law.

Former personnel of the Pine Gap base in central Australia told the Age newspaper in July that one of the base's primary functions was to locate radio signals in the eastern hemisphere, with the information gathered fed through to the US drone programme.

According to an ongoing investigation by the Bureau of Investigative Journalism (BIJ) in London, there have been 371 US drone strikes in Pakistan alone since 2004, resulting in up to 3,584 killings, the majority of whom were militants. But the BIJ also estimates up to 928 civilians have been killed in the Pakistan programme, with up to 195 of those children.

The letter says if the Pine Gap facility was engaged in supplying location data for drone strikes "these allegations raise serious concerns about the complicity of Australian officials in civilian deaths caused by the US drone strikes".

It continues: "In particular we are concerned that Australian officials may have facilitated targeted killing in violation of international humanitarian law and international human rights law."

It requests that the inquiry examine the extent to which intelligence from Pine Gap was used in 25 case studies being examined by the panel, to look at the "nature of co-operation" between Australian and US officials in providing locational data used in targeting, and the basis on which any co-operation is lawful.

"The aim of the inquiry is to shine the light of truth on the competing allegations that there are disproportionate civilian casualties on the one hand and that there are few or no civilian casualties on the other," Emmerson told the Guardian. "The critical lacuna in the debate that is currently taking place within the United Nations concerning the legality of drone strikes is the absence of independent, objective verification of the facts."

"The position of the government of Pakistan is quite clear. It does not consent to the use of drones by the United States on its territory and it considers this to be a violation of Pakistan's sovereignty and territorial integrity," he said.

He added: "As a matter of international law the US drone campaign in Pakistan is therefore being conducted without the consent of the elected representatives of the people, or the legitimate government of the state. It involves the use of force on the territory of another state without its consent and is therefore a violation of Pakistan's sovereignty."

In July, documents released by the National Security Agency whistleblower Edward Snowden indicated that the Pine Gap base was one of four locations in Australia used as part of the NSA's XKeyscore internet surveillance programme. This, according to the documents, allows analysts to search through vast databases containing emails, online chats and the browser history of millions of individuals.

A spokeswoman for the Department of Defence said it they could not comment on intelligence matters but added: "Australia works with the intelligence agencies of our close ally and closest partners to protect our country from threats such as terrorism. All such activities are conducted in strict accordance with Australian law."